Having managed to offend the Kreetassans yet again while negotiating for a much-needed plasma injector, Archer returns to Enterprise frustrated. Things get even worse when he learns that Porthos picked up some kind of pathogen on the Kreetassan homeworld, and must be confined to sickbay. Unfortunately, Porthos' condition only worsens, and Dr. Phlox must prevent the beagle's auto-immune system from collapsing entirely. As Archer worries about the fate of his pet, T'Pol informs him that she has discovered the reason for the Kreetassans' anger. Apparently, Porthos urinated on one of the 300-year-old Alvera trees — which are considered cultural treasures — outside the Hall of Diplomacy. In order to receive the plasma injector for Enterprise, the captain will most likely have to perform several acts of contrition. This infuriates Archer even more — especially since he thinks the Kreetassans should have known there was a pathogen in their atmosphere that Porthos couldn't handle.
Frustrated, Archer decides to spend the night in sickbay to be near his pet. While there, he observes Phlox working on a cure, as well as performing odd personal grooming task and feeding his menagerie of creatures. Unable to sleep, Archer goes to the ship's gym to exercise, where he encounters T'Pol. As the two run side by side on treadmills, they argue over how to deal with the Kreetassans. T'Pol thinks Archer is, once again, allowing his human feelings to get in the way of his duty, while Archer is irritated by T'Pol's unsympathetic stance regarding Porthos. In the middle of their work-out, Hoshi summons the pair with the list of demands from the Kreetassans. Archer reads them and storms back to sickbay, disgusted. Unfortunately, Porthos' condition is even worse — the pooch has gone into anaphylactic shock, and his body is rejecting Phlox's treatment.
As the night creeps on, Archer grows more exhausted and worried. Phlox suggests that perhaps the sexual tension between the captain and T'Pol is contributing to his frustration, a notion that Archer quickly dismisses. Later that night, Archer dreams of a funeral for Porthos and an intimate moment with T'Pol. When he awakens, Porthos still isn't doing well — Phlox's treatment was partially effective, but the beagle's pituitary gland is severely damaged. Phlox must now perform an intricate underwater operation to replace Porthos' pituitary gland with that of a Calrissian chameleon. During the operation, the doctor and the captain discuss Archer's possible attraction to T'Pol, Phlox's extended family and cultural differences. This conversation seems to give Archer a greater understanding of other cultures in general ... and why he must apologize to the Kreetassans.
Returning to the Kreetassan homeworld, Archer performs a bizarre ritual that involves chopping off pieces of a tree trunk and arranging them in a certain pattern. The apology pleases the Kreetassans enough to earn Enterprise the plasma injector — as well as a couple of spares. Upon returning to Enterprise, Archer makes an apology of a more personal nature to T'Pol, and tells her that he's sorry for the recent conflicts between them. The apparent sexual tension between them remains unaddressed, however.
Returning to sickbay, Archer learns that the transplant went perfectly, and Porthos is on the road to recovery. Overjoyed, the captain thanks Phlox, and takes his pet home.